메뉴 건너뛰기




Volumn 45, Issue D1, 2017, Pages D408-D414

HIPPIE v2.0: Enhancing meaningfulness and reliability of protein-protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; INFORMATION PROCESSING; INFORMATION RETRIEVAL; PROTEIN PROTEIN INTERACTION; RELIABILITY; SOFTWARE; BIOLOGY; HUMAN; PROCEDURES; PROTEIN ANALYSIS; PROTEIN DATABASE; REPRODUCIBILITY; WEB BROWSER;

EID: 85016100476     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw985     Document Type: Article
Times cited : (346)

References (52)
  • 6
    • 84908086793 scopus 로고    scopus 로고
    • Predicting disease associations via biological network analysis
    • Sun, K., Gonçalves, J.P., Larminie, C. and Przulj, N. (2014) Predicting disease associations via biological network analysis. BMC Bioinformatics, 15, 304.
    • (2014) BMC Bioinformatics , vol.15 , pp. 304
    • Sun, K.1    Gonçalves, J.P.2    Larminie, C.3    Przulj, N.4
  • 7
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks
    • Hart, G.T., Ramani, A.K. and Marcotte, E.M. (2006) How complete are current yeast and human protein-interaction networks. Genome Biol., 7, 120.
    • (2006) Genome Biol. , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 9
    • 0035212065 scopus 로고    scopus 로고
    • Is there a bias in proteome research?
    • Mrowka, R., Patzak, A. and Herzel, H. (2001) Is there a bias in proteome research? Genome Res., 11, 1971-1973.
    • (2001) Genome Res. , vol.11 , pp. 1971-1973
    • Mrowka, R.1    Patzak, A.2    Herzel, H.3
  • 10
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • Von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 11
    • 79960245388 scopus 로고    scopus 로고
    • Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor
    • Bisson, N., James, D.A., Ivosev, G., Tate, S.A., Bonner, R., Taylor, L. and Pawson, T. (2011) Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Nat. Biotechnol., 29, 653-658.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 653-658
    • Bisson, N.1    James, D.A.2    Ivosev, G.3    Tate, S.A.4    Bonner, R.5    Taylor, L.6    Pawson, T.7
  • 12
    • 34047168855 scopus 로고    scopus 로고
    • Comparison of human protein-protein interaction maps
    • Futschik, M.E., Chaurasia, G. and Herzel, H. (2007) Comparison of human protein-protein interaction maps. Bioinformatics, 23, 605-611.
    • (2007) Bioinformatics , vol.23 , pp. 605-611
    • Futschik, M.E.1    Chaurasia, G.2    Herzel, H.3
  • 13
    • 84897102242 scopus 로고    scopus 로고
    • Bias tradeoffs in the creation and analysis of protein-protein interaction networks
    • Gillis, J., Ballouz, S. and Pavlidis, P. (2014) Bias tradeoffs in the creation and analysis of protein-protein interaction networks. J. Proteomics, 100, 44-54.
    • (2014) J. Proteomics , vol.100 , pp. 44-54
    • Gillis, J.1    Ballouz, S.2    Pavlidis, P.3
  • 14
    • 84941004380 scopus 로고    scopus 로고
    • Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types
    • Schaefer, M.H., Serrano, L. and Andrade-Navarro, M.A. (2015) Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. Front. Genet., 6, 260.
    • (2015) Front. Genet. , vol.6 , pp. 260
    • Schaefer, M.H.1    Serrano, L.2    Andrade-Navarro, M.A.3
  • 24
    • 79955667824 scopus 로고    scopus 로고
    • The biomolecular interaction network database in PSI-MI 2.5
    • Isserlin, R., El-Badrawi, R.A. and Bader, G.D. (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford), 2011, baq037.
    • (2011) Database (Oxford) , vol.2011 , pp. baq037
    • Isserlin, R.1    El-Badrawi, R.A.2    Bader, G.D.3
  • 32
    • 85032149838 scopus 로고    scopus 로고
    • Gene set to Diseases (GS2D): Disease enrichment analysis on human gene sets with literature data
    • In press
    • Andrade-Navarro, M.A. and Fontaine, J.F. (2016) Gene set to Diseases (GS2D): disease enrichment analysis on human gene sets with literature data. Genomics and Computational Biology, In press.
    • (2016) Genomics and Computational Biology
    • Andrade-Navarro, M.A.1    Fontaine, J.F.2
  • 33
    • 84976875034 scopus 로고    scopus 로고
    • PANTHER version 10: Expanded protein families and functions, and analysis tools
    • Mi, H., Poudel, S., Muruganujan, A., Casagrande, J.T. and Thomas, P.D. (2016) PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res., 44, D336-D342.
    • (2016) Nucleic Acids Res. , vol.44 , pp. D336-D342
    • Mi, H.1    Poudel, S.2    Muruganujan, A.3    Casagrande, J.T.4    Thomas, P.D.5
  • 35
    • 84879955888 scopus 로고    scopus 로고
    • A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
    • Lan, A., Ziv-Ukelson, M. and Yeger-Lotem, E. (2013) A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. Bioinformatics, 29, i210-i216.
    • (2013) Bioinformatics , vol.29 , pp. i210-i216
    • Lan, A.1    Ziv-Ukelson, M.2    Yeger-Lotem, E.3
  • 37
    • 84864470208 scopus 로고    scopus 로고
    • SteinerNet: A web server for integrating 'omic' data to discover hidden components of response pathways
    • Tuncbag, N., McCallum, S., Huang, S.-S.C. and Fraenkel, E. (2012) SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res., 40, W505-W509.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W505-W509
    • Tuncbag, N.1    McCallum, S.2    Huang, S.-S.C.3    Fraenkel, E.4
  • 38
    • 84903384845 scopus 로고    scopus 로고
    • Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases
    • Barshir, R., Shwartz, O., Smoly, I.Y. and Yeger-Lotem, E. (2014) Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput. Biol., 10, e1003632.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003632
    • Barshir, R.1    Shwartz, O.2    Smoly, I.Y.3    Yeger-Lotem, E.4
  • 39
    • 84959903835 scopus 로고    scopus 로고
    • Cytoscape.js: A graph theory library for visualisation and analysis
    • Franz, M., Lopes, C.T., Huck, G., Dong, Y., Sumer, O. and Bader, G.D. (2016) Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics, 32, 309-311.
    • (2016) Bioinformatics , vol.32 , pp. 309-311
    • Franz, M.1    Lopes, C.T.2    Huck, G.3    Dong, Y.4    Sumer, O.5    Bader, G.D.6
  • 42
    • 84976905746 scopus 로고    scopus 로고
    • Integrated interactions database: Tissue-specific view of the human and model organism interactomes
    • Kotlyar, M., Pastrello, C., Sheahan, N. and Jurisica, I. (2016) Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Res., 44, D536-D541.
    • (2016) Nucleic Acids Res. , vol.44 , pp. D536-D541
    • Kotlyar, M.1    Pastrello, C.2    Sheahan, N.3    Jurisica, I.4
  • 44
    • 84979866839 scopus 로고    scopus 로고
    • MyProteinNet: Build up-to-date protein interaction networks for organisms, tissues and user-defined contexts
    • Basha, O., Flom, D., Barshir, R., Smoly, I., Tirman, S. and Yeger-Lotem, E. (2015) MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. Nucleic Acids Res., 43, W258-W263.
    • (2015) Nucleic Acids Res. , vol.43 , pp. W258-W263
    • Basha, O.1    Flom, D.2    Barshir, R.3    Smoly, I.4    Tirman, S.5    Yeger-Lotem, E.6
  • 46
    • 84968912147 scopus 로고    scopus 로고
    • Integration of multiple biological features yields high confidence human protein interactome
    • Karagoz, K., Sevimoglu, T. and Arga, K.Y. (2016) Integration of multiple biological features yields high confidence human protein interactome. J. Theor. Biol., 403, 85-96.
    • (2016) J. Theor. Biol. , vol.403 , pp. 85-96
    • Karagoz, K.1    Sevimoglu, T.2    Arga, K.Y.3
  • 47
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • Vidal, M., Cusick, M.E. and Barabási, A.-L. (2011) Interactome networks and human disease. Cell, 144, 986-998.
    • (2011) Cell , vol.144 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 48
    • 84903388648 scopus 로고    scopus 로고
    • Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways
    • Schaefer, M.H., Yang, J.-S., Serrano, L. and Kiel, C. (2014) Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways. PLoS Comput. Biol., 10, e1003659.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003659
    • Schaefer, M.H.1    Yang, J.-S.2    Serrano, L.3    Kiel, C.4
  • 49
    • 84891845335 scopus 로고    scopus 로고
    • Integration of protein abundance and structure data reveals competition in the ERBB signaling network
    • Kiel, C., Verschueren, E., Yang, J.-S. and Serrano, L. (2013) Integration of protein abundance and structure data reveals competition in the ErbB signaling network. Sci. Signal., 6, ra109.
    • (2013) Sci. Signal. , vol.6 , pp. ra109
    • Kiel, C.1    Verschueren, E.2    Yang, J.-S.3    Serrano, L.4
  • 52
    • 30944447568 scopus 로고    scopus 로고
    • The extracellular signal-regulated kinase: Multiple substrates regulate diverse cellular functions
    • Yoon, S. and Seger, R. (2006) The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions. Growth Factors, 24, 21-44.
    • (2006) Growth Factors , vol.24 , pp. 21-44
    • Yoon, S.1    Seger, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.